Biology 335 - Molecular Genetics

Eukaryotic Gene Expression

Genome Organization
This will be a brief introduction to eukaryotic gene expression...as a consequence of the brevity of this discussion, we will focus our attention on the differences between prokaryotes and eukaryotes...

Organization of the Genome
Prokaryotes

Bare DNA
Accessible to the txn machinery

Ground State is ON

Regulation turns genes OFF
Negative Regulation
Eukaryotes

CHROMATIN (DNA - protein complex)
inaccessible to the txn apparatus

Ground State is OFF

Regulation turns genes ON
Positive Regulation
Recall our discussion of the Hierarchical Organization of the genome in eukaryotes...

Packaging of the genome into free nucleosomes (beads-on-a-string) allows the txn apparatus to access the template and renders sequences in this configuration TRANSCRIPTIONALLY ACTIVE

Packing of the nucleosomes into the solenoid configuration blocks access to the packaged template.
Therefore the solenoid configuration is TRANSCRIPTIONALLY INACTIVE.

We can use a simple tool (sensitivity to DNase I degradation)
to distinguish between these two packaging levels and their associated transcriptional status.
Genomic sequences packaged into free nucleosomes are accessible to both transcription machinery and DNase I digestion Genomic sequences organized into the solenoid configuration are inaccessible to both transcription machinery and DNase I digestion.
Linker DNA is easily accessible to DNase I
SENSITIVE
digested to nucleosome cores

Transcriptionally Active
Linker DNA is highly packaged
inaccessible
INSENSITIVE to DNase I

Transcriptionally Inactive
The solenoid configuration is held together by interactions between the unstructured N-terminal domains of the core histones of adjacent nucleosomes.
The stability of the solenoid can be regulated by covalent modification of these N-terminal domains

Histone Acetyl Transferases (HAT) transfer an acetyl group onto the N-terminal domains
blocking their interactionl, destabilizing the solenoid configuration
making the Genomic DNA accessible to the transcription machinery and DNase I.

Histone DeAcetylases (HDAc) remove the acetyl group from the N-terminal domains
promoting their interaction, stabilizing the solenoid configuration
making the Genomic DNA inaccessible to the transcription machinery and DNase I.
Ground State

Unacetylated
Solenoid

Transcriptionally INACTIVE
DNase I resistant
Activated

Acetylated
Free Nucleosomes

Transcritionally ACTIVE
DNase I sensitive
go to
Eukaryotic Transcription II